I can get 3D weapon models to show up no problem in Doom/Doom II, but when I do the same thing in Heretic, they won't show. I know my .DEF is loading because the sprites will disappear during the frames I have overwritten with my model. but the model just won't show up. I can even rename and put my heretic models into my doom pk3, and they show up fine.

You should remove that intermediate HereticVRWeapons folder. The zip loader cannot decide in this case whether to treat it as a container or as a genuine part of the mod.But even after that I do not see any models. They are just empty, it seems.

I'll follow your first suggestion. So when you boot them up, does the base frame for the crossbow show? Is it possible that someone borked the code, and 3D weapons scale 100 times smaller or something? We know it's worked in the past or people wouldn't have made weapon packs. Here's a youtube video from 3 years ago that has 3D weapon models: https://www.youtube.com/watch?v=b9b8hpEKHLs